1p1c - Revision history

OCA at 08:04, 14 February 2024

OCA — Wed, 14 Feb 2024 08:04:28 GMT

←Older revision		Revision as of 08:04, 14 February 2024
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	<StructureSection load='1p1c' size='340' side='right'caption='[[1p1c]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1p1c' size='340' side='right'caption='[[1p1c]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1p1c]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Buffalo_rat Buffalo rat~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P1C OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1P1C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1p1c]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P1C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P1C FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GD3:GADOLINIUM+ION'>GD3</scene>~~, ~~<scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.5Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1p1b\|1p1b]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GD3:GADOLINIUM+ION'>GD3</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>GAMT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~10116 Buffalo rat])</td~~><~~/tr>~~	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1p1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p1c OCA], [https://pdbe.org/1p1c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p1c RCSB], [https://www.ebi.ac.uk/pdbsum/1p1c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p1c ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[http~~:~~//en.wikipedia.org/wiki/Guanidinoacetate_N~~-~~methyltransferase Guanidinoacetate N~~-~~methyltransferase], with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=2.1.1.2 2.1.1.2]~~ </~~span~~></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1p1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p1c OCA], [~~http~~://pdbe.org/1p1c PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1p1c RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1p1c PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1p1c ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/GAMT_RAT GAMT_RAT]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1p1c ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1p1c ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Guanidinoacetate methyltransferase (GAMT) is the enzyme that catalyzes the last step of creatine biosynthesis. The enzyme is found in abundance in the livers of all vertebrates. Recombinant rat liver GAMT truncated at amino acid 37 from the N-terminus has been crystallized with S-adenosylhomocysteine (SAH) in a monoclinic modification and the crystal structure has been determined at 2.8 A resolution. There are two dimers in the crystallographic asymmetric unit. Each dimer has non-crystallographic twofold symmetry and is related to the other dimer by pseudo-4(3) symmetry along the crystallographic b axis. The overall structure of GAMT crystallized in the monoclinic modification is quite similar to the structure observed in the tetragonal modification [Komoto et al. (2002), J. Mol. Biol. 320, 223-235], with the exception of the loop containing Tyr136. In the monoclinic modification, the loops in three of the four subunits have a catalytically unfavorable conformation and the loop of the fourth subunit has a catalytically favorable conformation as observed in the crystals of the tetragonal modification. From the structures in the monoclinic and tetragonal modifications, we can explain why the Y136F mutant enzyme retains considerable catalytic activity while the Y136V mutant enzyme loses the catalytic activity. The crystal structure of a Gd derivative of the tetragonal modification has also been determined. By comparing the Gd-derivative structure with the native structures in the tetragonal and the monoclinic modifications, useful characteristic features of Gd-ion binding for application in protein crystallography have been observed. Gd ions can bind to proteins without changing the native protein structures and Gd atoms produce strong anomalous dispersion signals from Cu Kalpha radiation; however, Gd-ion binding to protein requires a relatively specific geometry.
-
-	Monoclinic guanidinoacetate methyltransferase and gadolinium ion-binding characteristics.,Komoto J, Takata Y, Yamada T, Konishi K, Ogawa H, Gomi T, Fujioka M, Takusagawa F Acta Crystallogr D Biol Crystallogr. 2003 Sep;59(Pt 9):1589-96. Epub 2003, Aug 19. PMID:12925789<ref>PMID:12925789</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1p1c" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Buffalo rat]]
-	[[Category: Guanidinoacetate N-methyltransferase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Komoto, J~~]]	+	[[Category: Rattus norvegicus]]
-	[[Category: ~~Takusagawa, F~~]]	+	[[Category: Komoto J]]
-	[[Category: ~~Gd ion]]~~	+	[[Category: Takusagawa F]]
-	~~[[Category: Guanidinoacetate methyltransferase]]~~	+
-	~~[[Category: Methyltransferase]]~~	+
-	~~[[Category: S-adenosylhomocysteine]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:20, 9 December 2020

OCA — Wed, 09 Dec 2020 07:20:57 GMT

←Older revision		Revision as of 07:20, 9 December 2020
Line 1:		Line 1:

	==Guanidinoacetate Methyltransferase with Gd ion==		==Guanidinoacetate Methyltransferase with Gd ion==
-	<StructureSection load='1p1c' size='340' side='right' caption='[[1p1c]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='1p1c' size='340' side='right'caption='[[1p1c]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1p1c]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P1C OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1P1C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1p1c]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P1C OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1P1C FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GD3:GADOLINIUM+ION'>GD3</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GD3:GADOLINIUM+ION'>GD3</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p1b\|1p1b]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1p1b\|1p1b]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GAMT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GAMT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Guanidinoacetate_N-methyltransferase Guanidinoacetate N-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.2 2.1.1.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Guanidinoacetate_N-methyltransferase Guanidinoacetate N-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.2 2.1.1.2] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1p1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p1c OCA], [http://pdbe.org/1p1c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1p1c RCSB], [http://www.ebi.ac.uk/pdbsum/1p1c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1p1c ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1p1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p1c OCA], [http://pdbe.org/1p1c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1p1c RCSB], [http://www.ebi.ac.uk/pdbsum/1p1c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1p1c ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p1/1p1c_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p1/1p1c_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 35:		Line 35:
	[[Category: Buffalo rat]]		[[Category: Buffalo rat]]
	[[Category: Guanidinoacetate N-methyltransferase]]		[[Category: Guanidinoacetate N-methyltransferase]]
		+	[[Category: Large Structures]]
	[[Category: Komoto, J]]		[[Category: Komoto, J]]
	[[Category: Takusagawa, F]]		[[Category: Takusagawa, F]]

OCA at 08:22, 12 October 2017

OCA — Thu, 12 Oct 2017 08:22:47 GMT

←Older revision		Revision as of 08:22, 12 October 2017
Line 1:		Line 1:
		+
	==Guanidinoacetate Methyltransferase with Gd ion==		==Guanidinoacetate Methyltransferase with Gd ion==
	<StructureSection load='1p1c' size='340' side='right' caption='[[1p1c]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1p1c' size='340' side='right' caption='[[1p1c]], [[Resolution\|resolution]] 2.50Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GAMT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GAMT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Guanidinoacetate_N-methyltransferase Guanidinoacetate N-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.2 2.1.1.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Guanidinoacetate_N-methyltransferase Guanidinoacetate N-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.2 2.1.1.2] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1p1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p1c OCA], [http://pdbe.org/1p1c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1p1c RCSB], [http://www.ebi.ac.uk/pdbsum/1p1c PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1p1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p1c OCA], [http://pdbe.org/1p1c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1p1c RCSB], [http://www.ebi.ac.uk/pdbsum/1p1c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1p1c ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1p1c ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:36, 11 September 2015

OCA — Fri, 11 Sep 2015 07:36:45 GMT

←Older revision		Revision as of 07:36, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1p1c' size='340' side='right' caption='[[1p1c]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1p1c' size='340' side='right' caption='[[1p1c]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1p1c]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rattus_norvegicus Rattus norvegicus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P1C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1P1C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1p1c]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P1C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1P1C FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GD3:GADOLINIUM+ION'>GD3</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GD3:GADOLINIUM+ION'>GD3</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p1b\|1p1b]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p1b\|1p1b]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GAMT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 ~~Rattus norvegicus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GAMT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Guanidinoacetate_N-methyltransferase Guanidinoacetate N-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.2 2.1.1.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Guanidinoacetate_N-methyltransferase Guanidinoacetate N-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.2 2.1.1.2] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1p1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p1c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1p1c RCSB], [http://www.ebi.ac.uk/pdbsum/1p1c PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1p1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p1c OCA], [http://pdbe.org/1p1c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1p1c RCSB], [http://www.ebi.ac.uk/pdbsum/1p1c PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 27:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1p1c" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Buffalo rat]]
	[[Category: Guanidinoacetate N-methyltransferase]]		[[Category: Guanidinoacetate N-methyltransferase]]
-	[[Category: Rattus norvegicus]]
	[[Category: Komoto, J]]		[[Category: Komoto, J]]
	[[Category: Takusagawa, F]]		[[Category: Takusagawa, F]]

OCA at 06:52, 6 January 2015

OCA — Tue, 06 Jan 2015 06:52:53 GMT

←Older revision		Revision as of 06:52, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1p1c]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P1C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1P1C FirstGlance]. <br>		<table><tr><td colspan='2'>[[1p1c]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P1C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1P1C FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GD3:GADOLINIUM+ION'>GD3</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GD3:GADOLINIUM+ION'>GD3</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p1b\|1p1b]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p1b\|1p1b]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GAMT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GAMT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Guanidinoacetate_N-methyltransferase Guanidinoacetate N-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.2 2.1.1.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Guanidinoacetate_N-methyltransferase Guanidinoacetate N-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.2 2.1.1.2] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1p1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p1c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1p1c RCSB], [http://www.ebi.ac.uk/pdbsum/1p1c PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1p1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p1c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1p1c RCSB], [http://www.ebi.ac.uk/pdbsum/1p1c PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	[[Category: Guanidinoacetate N-methyltransferase]]		[[Category: Guanidinoacetate N-methyltransferase]]
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
-	[[Category: Komoto, J.]]	+	[[Category: Komoto, J]]
-	[[Category: Takusagawa, F.]]	+	[[Category: Takusagawa, F]]
	[[Category: Gd ion]]		[[Category: Gd ion]]
	[[Category: Guanidinoacetate methyltransferase]]		[[Category: Guanidinoacetate methyltransferase]]

OCA at 22:17, 28 September 2014

OCA — Sun, 28 Sep 2014 22:17:51 GMT

←Older revision		Revision as of 22:17, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1p1c.~~png~~\|~~left~~\|200px]]	+	==Guanidinoacetate Methyltransferase with Gd ion==
		+	<StructureSection load='1p1c' size='340' side='right' caption='[[1p1c]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1p1c]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P1C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1P1C FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GD3:GADOLINIUM+ION'>GD3</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p1b\|1p1b]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GAMT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Guanidinoacetate_N-methyltransferase Guanidinoacetate N-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.2 2.1.1.2] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1p1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p1c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1p1c RCSB], [http://www.ebi.ac.uk/pdbsum/1p1c PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p1/1p1c_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Guanidinoacetate methyltransferase (GAMT) is the enzyme that catalyzes the last step of creatine biosynthesis. The enzyme is found in abundance in the livers of all vertebrates. Recombinant rat liver GAMT truncated at amino acid 37 from the N-terminus has been crystallized with S-adenosylhomocysteine (SAH) in a monoclinic modification and the crystal structure has been determined at 2.8 A resolution. There are two dimers in the crystallographic asymmetric unit. Each dimer has non-crystallographic twofold symmetry and is related to the other dimer by pseudo-4(3) symmetry along the crystallographic b axis. The overall structure of GAMT crystallized in the monoclinic modification is quite similar to the structure observed in the tetragonal modification [Komoto et al. (2002), J. Mol. Biol. 320, 223-235], with the exception of the loop containing Tyr136. In the monoclinic modification, the loops in three of the four subunits have a catalytically unfavorable conformation and the loop of the fourth subunit has a catalytically favorable conformation as observed in the crystals of the tetragonal modification. From the structures in the monoclinic and tetragonal modifications, we can explain why the Y136F mutant enzyme retains considerable catalytic activity while the Y136V mutant enzyme loses the catalytic activity. The crystal structure of a Gd derivative of the tetragonal modification has also been determined. By comparing the Gd-derivative structure with the native structures in the tetragonal and the monoclinic modifications, useful characteristic features of Gd-ion binding for application in protein crystallography have been observed. Gd ions can bind to proteins without changing the native protein structures and Gd atoms produce strong anomalous dispersion signals from Cu Kalpha radiation; however, Gd-ion binding to protein requires a relatively specific geometry.

-	~~{{STRUCTURE_1p1c\| PDB=1p1c \| SCENE= }}~~	+	Monoclinic guanidinoacetate methyltransferase and gadolinium ion-binding characteristics.,Komoto J, Takata Y, Yamada T, Konishi K, Ogawa H, Gomi T, Fujioka M, Takusagawa F Acta Crystallogr D Biol Crystallogr. 2003 Sep;59(Pt 9):1589-96. Epub 2003, Aug 19. PMID:12925789<ref>PMID:12925789</ref>

-	~~===Guanidinoacetate Methyltransferase with Gd ion===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12925789}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1p1c]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Rattus_norvegicus Rattus norvegicus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1P1C OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012925789<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Guanidinoacetate N-methyltransferase]]		[[Category: Guanidinoacetate N-methyltransferase]]
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]

OCA: Protected "1p1c" [edit=sysop:move=sysop]

OCA — Wed, 12 Dec 2012 21:56:16 GMT

Protected "1p1c" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:56, 12 December 2012

OCA at 21:56, 12 December 2012

OCA — Wed, 12 Dec 2012 21:56:12 GMT

←Older revision		Revision as of 21:56, 12 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1p1c.png\|left\|200px]]		[[Image:1p1c.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1p1c", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1p1c\| PDB=1p1c \| SCENE= }}		{{STRUCTURE_1p1c\| PDB=1p1c \| SCENE= }}

	===Guanidinoacetate Methyltransferase with Gd ion===		===Guanidinoacetate Methyltransferase with Gd ion===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12925789}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12925789 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12925789}}		{{ABSTRACT_PUBMED_12925789}}

	==About this Structure==		==About this Structure==
-	~~1P1C~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P1C OCA].	+	[[1p1c]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P1C OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12925789~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012925789</ref><references group="xtra"/>
	[[Category: Guanidinoacetate N-methyltransferase]]		[[Category: Guanidinoacetate N-methyltransferase]]
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
Line 32:		Line 20:
	[[Category: Methyltransferase]]		[[Category: Methyltransferase]]
	[[Category: S-adenosylhomocysteine]]		[[Category: S-adenosylhomocysteine]]
-		+	[[Category: Transferase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 17:14:33 2009''~~	+

OCA at 15:14, 17 February 2009

OCA — Tue, 17 Feb 2009 15:14:33 GMT

←Older revision		Revision as of 15:14, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1P1C is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P1C OCA].	+	1P1C is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P1C OCA].

	==Reference==		==Reference==
-	Monoclinic guanidinoacetate methyltransferase and gadolinium ion-binding characteristics., Komoto J, Takata Y, Yamada T, Konishi K, Ogawa H, Gomi T, Fujioka M, Takusagawa F, Acta Crystallogr D Biol Crystallogr. 2003 Sep;59(Pt 9):1589-96. Epub 2003, Aug 19. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/12925789 12925789]~~	+	<ref group="xtra">PMID:12925789</ref><references group="xtra"/>
	[[Category: Guanidinoacetate N-methyltransferase]]		[[Category: Guanidinoacetate N-methyltransferase]]
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
-	[[Category: Single protein]]
	[[Category: Komoto, J.]]		[[Category: Komoto, J.]]
	[[Category: Takusagawa, F.]]		[[Category: Takusagawa, F.]]
Line 34:		Line 33:
	[[Category: S-adenosylhomocysteine]]		[[Category: S-adenosylhomocysteine]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 00~~:07:~~00 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:14:33 2009''

OCA at 21:07, 28 July 2008

OCA — Mon, 28 Jul 2008 21:07:07 GMT

←Older revision		Revision as of 21:07, 28 July 2008
Line 1:		Line 1:
-	[[Image:1p1c.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1p1c.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_1p1c\| PDB=1p1c \| SCENE= }}		{{STRUCTURE_1p1c\| PDB=1p1c \| SCENE= }}

-	~~'''~~Guanidinoacetate Methyltransferase with Gd ion~~'''~~	+	===Guanidinoacetate Methyltransferase with Gd ion===


-	~~==Overview==~~	+	<!--
-	~~Guanidinoacetate methyltransferase (GAMT) is the enzyme that catalyzes the last step of creatine biosynthesis.~~ The ~~enzyme is found in abundance in~~ the ~~livers of all vertebrates. Recombinant rat liver GAMT truncated at amino acid 37 from~~ the ~~N-terminus has been crystallized with S-adenosylhomocysteine~~ (~~SAH) in a monoclinic modification and the crystal structure has been determined~~ at 2.~~8 A resolution~~. ~~There are two dimers in the crystallographic asymmetric unit. Each dimer has non-crystallographic twofold symmetry and is related to the other dimer by pseudo-4(3~~) ~~symmetry along the crystallographic b axis. The overall structure of GAMT crystallized in the monoclinic modification~~ is ~~quite similar to~~ the ~~structure observed in the tetragonal modification [Komoto et al~~. ~~(2002), J. Mol. Biol. 320, 223~~-235], with the exception of the loop containing Tyr136. In the monoclinic modification, the loops in three of the four subunits have a catalytically unfavorable conformation and the loop of the fourth subunit has a catalytically favorable conformation as observed in the crystals of the tetragonal modification. From the structures in the monoclinic and tetragonal modifications, we can explain why the Y136F mutant enzyme retains considerable catalytic activity while the Y136V mutant enzyme loses the catalytic activity. The crystal structure of a Gd derivative of the tetragonal modification has also been determined. By comparing the Gd-derivative structure with the native structures in the tetragonal and the monoclinic modifications, useful characteristic features of Gd-ion binding for application in protein crystallography have been observed. Gd ions can bind to proteins without changing the native protein structures and Gd atoms produce strong anomalous dispersion signals from Cu Kalpha radiation; however, Gd-ion binding to protein requires a relatively specific geometry.	+	The line below this paragraph, {{ABSTRACT_PUBMED_12925789}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 12925789 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_12925789}}

	==About this Structure==		==About this Structure==
Line 29:		Line 33:
	[[Category: Methyltransferase]]		[[Category: Methyltransferase]]
	[[Category: S-adenosylhomocysteine]]		[[Category: S-adenosylhomocysteine]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May 3 04~~:33:29 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 00:07:00 2008''